A method is known in which, when a process of irradiating a sample with focused ion beams to form a thin sample or the like is performed, using a detection image of a secondary electron or the like, a predetermined place is grasped by pattern matching which uses a mark for drift correction on a surface of the sample as a landmark and a sample thickness is measured by detection of electron transmittance or the like at the predetermined place (for instance, see JP-A-2004-361140).